Only in Darkness
by Goldenlion3
Summary: Fresh recruits join the Enterprise and help Captain Kirk capture Khan. Will Khan alter their view of aliens and learn what it means to be accepted and have a family? Their loyalties will get tested through loss of friends, love, and betrayal, to see where their hearts lie.
1. Chapter 1

**Chapter One**

It was supposed to be one of the happiest days of my life, and it was for a few hours. I remember waking up in my dorm that had all ready been packed. All that remained was a silly little note to the incoming juniors that would take our room, and a few boxes of my stuff that hadn't been moved out yet. I looked over at my room mate, Katie, as usual she was talking in her sleep, "Kir...Kir..Kirk, wil..will ya..," she sighed and turned over. Ever since Captain Kirk had been named as the captain of the Enterprise, the premiere ship and the one we would hopefully be transferred to, she developed a major crush. Captain Kirk was quite handsome, he had piercing ice blue eyes and like all members of the Enterprise was in great physical condition, but he was the captain and had quite a reputation of being a player. I was very worried for Katie, she and I would defiantly get onto the Enterprise (because of our outstanding grades and in no part to Katie's excellent flirting to our arithmetic teacher) but when she did, she would no doubt get attached to Captain Kirk and there is no telling how that would turn out.

I went over to wake Katie up and then take a shower. All I could think about was graduation. I kept picturing myself tripping and making a fool of myself in front of everyone. And there really was everyone there, some representative from each of the ships, at least 200 alumni, and of course every relative of the graduates.

Starfleet Academy was the highest university there is. Just think of it as the school that had the highest student in every grade school, the prodigy that everyone envied, all of them gathered together and taught to the maximum. We were to become the people of tomorrow, the leaders of all our peers, the future superstars, and a bunch of other bull shit like that which would probably said at least three times in the graduation speeches. I was not looking forward to it, though the after parties should be fun. Besides for our intellect, we were also know for our rather luxurious and insane parties. There were three that I had planned on going to.

I stepped out of the shower and looked at myself in the mirror. Despite my medical training, I had managed to gain some muscle. My arms and chest were sculpted and just slightly defined. My legs were more lean, and had a higher kick stored in them then before I entered the academy. Even my face looked different, my childhood freckles had faded, though still visible, and my cheekbones were more prominent. The only thing that had stayed the same was my hair. It was still as long (or longer) as when I had walked the halls freshman year, though I did occasionally died the ends purple for weekends and parties.

This will certainly be a shock for my parents. The last time I saw them was when they helped to move me in, four years ago. I got the occasional email update, praising my brother's achievement in this new science exploration ship, very cutting edge. They were always traveling and working and didn't really have time for anything else.

"Katie? Are you up yet?" I asked as I left the bathroom to get my Starfleet uniform. I heard a nearly audible mumble in response. "Come on! We have to be ready by 11:30 so we can be down there by 12!" I grabbed my grey uniform dress, we got our coloured dresses when we got assigned a ship. But it wasn't like anyone was going to see the uniform under our white graduation dresses.

For the next hour I blowed dried my hair while Katie struggled to get up. The communicator started to ring, groaning I got up to answer it. Annoyed I answered it thinking it was some guy Katie gave our number to. "Hello?" Surprised I heard my mother's voice on the other end, "Hey sweetie, it turns out our ship won't be returning for another two months. So that means were going to miss your graduation-"

"But-" I said almost half heartily, wanting to believe it was some kind of sick, sick joke.

"-Love you sweetie! Have a great day! Email us what ship you get into! Lots of Love, mom and dad."

And then I realized the worst part of it. They prerecorded it. Not only did they miss one of the most important days of my life so far, but they didn't even have the half decency to tell me in person (or in person over the phone). "This is so unfair!" I thought. I couldn't help but break down into tears. I had worked four hard years on this stupid diploma! I studied and worked so hard! And for Christ's sake I was highest in my class! I really could care less about what a hydrocarbon was, and predicting the next trend in a quadratic formula was, I just wanted them to be proud of me, and I had obviously hadn't done a good enough job. Maybe if I was up to my brother's standards they would bother to skip a few days on their research.

I heard the water shut off in the bathroom and quickly tried to wipe away the tears. Katie stepped out and immediately noticed my face. "Oh Annagh! What happened?" Scrambling to think of a response I said, "Oh its just, ah, I'm really going to miss this place and having a dorm with you." I added a force smile at the end, hoping she wouldn't see though my mask. Even if this day was horrible for me, I shouldn't make it horrible for Katie too. "Aww so am I!" she didn't even notice as she pulled me into a hug, "but don't worry 'cuz I'm positive were going to make it to the Enterprise, and then I can marry Kirk and you can, ah, you can marry...SPOCK!" She seemed quite happy with our imagined futures. "Ah, no! That's gross!" Spock was my favorite teacher, but he was far from attractive and was emotionless, which everyone said made for bad..well...relations... "Well you are his 'favorite' student," She said mockingly. I gave her an eye roll and sat down to put on my makeup.

Katie insisted that she attach her false eyelashes before we go down, which of course made us nearly 10 minutes late. "Why do I even try?" I said as we tried to run down the flights of stairs in our giant heals and too long gowns. "Aw come on you know you love me." When we got to the doors to where everyone was lined up, we waited for Spock to turn his back and then gracefully slid into our positions. I was behind this really snooty girl, and in front of a boy that I had known since kindergarten but hadn't really 'known.' He tapped my shoulder and smiled as if to say 'good job,' I smiled back in return.

"Two new heart rates detected," Spock said from in front and in the middle of the two lines of graduates, "both over average." I cursed under my breath. "Lily!" he said as he turned around and headed in my direction. "Could this day get any worse?" I thought. As much as Spock was a good teacher and had a kind heart deep down, he honestly had no idea what made people annoyed or embarrassed, or any emotion for that matter. I heard a few snickers in the crowd, everyone was well aware that I was his favorite. "Can you explain why you and Mrs...," he said as he looked through his attendance sheet trying to find the other missing person," Mrs. Killian are late?" As much as I would love to say it was 'Mrs. Killian's fault, I didn't. "Ah just a later start, I guess..." He looked at me, "Hmm well I heard your parents will not be joining us, such a shame." I guess this day could get worse, a lot worse considering now everyone knew about my shitty parents. "Ah ya..," I mumbled and felt my face getting redder, "Ah work I guess." He 'Hmm'ed again and strode back to the front on the middle section. I felt the eyes of everyone around me, they were pitying me and feeling sorry, and I absolutely hated it.

After about an hour of practicing walking in a straight, we broke for lunch. The program started at three and was only a little past one now. Katie and I and our best friend, Leah all meet up our to eat in our usual spot, right under a genetically engineered oak tree in the outdoor student section. I knew they were gonna ask about the whole parent thing, so I had to think of something that would distract them for our short 30 minute lunch. "So what are you guys wearing, and what party do you think we should hit first?"

"Oh! I hear Jack's party is gonna be Amazing!" Katie was always up to date on who's who and all that type of stuff, "And to that one I'm wearing a little black dress, the one I showed you with the gold going down the side. "Wait who's Jack?" Leah on the other hand, was well not so much up to date, after all there are nearly 1000 students. Katie answered her question with an exaggerated eye roll, "Jack Hackney, of Course! He's the one thats always doing those back flips. And then after that I'm going to Daniel Basket's open house, apparently theres a mile long pool on his parent's apartment. And did I mention that this apartment is a whole floor on the Phoenix SkyScraper!" The Phoenix SkyScraper was one of the tallest buildings in the city and was known for the housing the most exclusive millionaires and captains. And was much like Daniel's Parent's house quite extravagant.

"Anyway I'm going to wear a royal blue cot-out dress and follow Katie drunkenly wherever she goes," I said. "Are you and Luke gonna meet us at our dorm or at Jack's?" I asked Leah. Luke and her had meet in one of their sophomore classes and had been going steady ever since, it was really quite adorable. "We'll meet you at your dorm but I'm staying sober, all night," Leah said. "Ha! Like that'll happen!" Katie was right, almost every party we went to this year Manya promise the same thing, but she always ended up in the morning with the same, if not worse, hangover. "Oh come on! Let it go! It's the last day that we can enjoy our Senoritis, we might as well enjoy it."

We spent the last 25 minutes taking about who will end up will who, and all other sorts of gossip, which felt so good after that embarrassment with Spock. As it neared closer to 3 all the family and special guests started to poor in. First was Katie's family complete with three great aunts and about a dozen various nieces, nephews, and otherwise. Of course she pulled me in and introduced me to everyone which was thoroughly exhausting. Then Leah's family arrived, I had known them since at least my third year at grammar school. I said hi to her mother and father, gracefully avoiding the question of my parent's absence, and of course talked to her brother. Manya and I had become so close over the years that he was practically my own brother, at least a lot better than my biological one.

Despite the excruciating small talk conversations and polite introductions, it was only just 2 o'clock, and I was exhausted. After prying two of Katie's nieces off my leg I slipped away to go upstairs. I decided to go where I usually went when Katie brought some guy over or if I had to escape a extremely boring lecture. There was a small little section right behind the biography of the old American presidents where the contractors seemed to have made a mistake. It was a little cuby whole that was perfect for escaping for a while. I closed my eyes and tried to focus on my breathing, I couldn't hold any type of typical social interaction sober, I was a true introvert if there ever was one. And just as I started to enjoy my peaceful silence, I heard a knock at the cuby entrance followed by a somewhat familiar voice, "Um, Lily?" Startled I looked up to see the guy who I stood in front of in the graduation line, and who's name I couldn't really remember. "Um hi?" This had to be one of the most awkward situations there was, a guy I knew but didn't really 'know' had just found me huddled in the fetal position behind a bunch of dusty old books when I should be socializing on one of the best days of my life. "Well this is uh-" Forgotten name boy interrupted me, "creppy, stalkerish, awkward? Yes I guess it is." He said as he sat down. I waited for him to continue but he didn't say a word just stared at me curiously. "Um..well I guess I should ask you how you found this place?" His smile grew a little bigger, I was starting to wish I knew a little bit more about him, "Well the same way you found it I guess, a long night in the library-an escape from a roommate-looking for a cozy place to curl up and while heading to the windows you just glimpse, just glimpse a little flicker of light. And of course if we choose a library as a place to get away, it is naturally in our nature to investigate this flicker of light." It was amazing it was almost like he was there when I discovered this place. Then I thought of a terrible thought, what if he was there, what if he was following me? "That's how I found the cuby whole through a little flicker of light from a silver star right in the corner," he pointed his finger to the spot where the star still stood, "and I thought I had find my little place in the world until a week later I came in around midnight to find a goldylocks sleeping in my corner." I laughed with him, if he was a stalker he was the type that was nice up until the end when he revealed he was a serial killer. "Anyway I thought I come up her to add a star to the collection, you know for the next generation of library wanderers."

It was rather perfect I thought later, not only did he totally distracts me from all the bull shit around me, but he made me laugh a little and had made me able to say goodbye to one of my own favorite places with out really trying. For that I was more than grateful, yet I still didn't even know his name.

We parted our ways as the time drew near to line up from graduation. Before I could ask him his name though, he had managed to disappear into the masses. "Lily are you coming?," it was Katie getting a little annoyed that I had left her to deal with her massive family alone, and would probably make her late again with my daydreaming. "Ya sure hold on..." I looked back over my shoulder before I totally left mysterious no name behind and followed Katie into the auditorium.


	2. Chapter 2

**I guess this is the part where I tell you I'm so sorry for updating so late...but school, and sports, and tumblr...**

**I really am sorry though. I'll be updating this friday and then in a regular retune of Wednesdays and Sundays. **

**So the story is gradually progressing, we will getting into the heavy action defiantly next chapter along with Khan's Introduction!**

**Remember I don't own any thing familiar, Read and Review, and most of all enjoy!**

The Graduation didn't disappoint, it was as long and boring as watching paint dry. If that paint was reapplied as each graduate's name was called. There must have been at least 25 dignified guest, those with the deepest pockets and biggest egos. And despite their successfulness, they could only comment on how "If we made it past Spock, we can make it anywhere." It was all very cliche and the speeches were really quite unhelpful in any foreseeable future. Honestly, who really cares who you were able to have the money to come back as the alumni, or that you haven't overdone anything to "remember were you are sitting right now." Especially when everyone's mind was on which ship there were going to get assigned to. As soon as the last middle aged alumni sat down and Admiral Pike stood up, I got a final massive surge of adrenaline and butter flies in my gut.

The famous Admiral Pike stood up smoothed his uniform and continued to the podium as only a solider would. He made a few opening remarks before listing the ships available for transfer. After about thirty somewhat important science, medical, rescue, and military ships, he announce the more A-list ships, making everyone shuffle and move forward in their seats. "Next are the ships, in size order, are the most crucial to Starflet. These ships go to the known and unknown ends of the universe to discover, explore, and make relations. Without these ships, Starflet would be some much less advanced and knowledgeable, and completely different than what we now today. These ships are, The USS Constitution commanded by Matthew Decker, The USS Excaliber commanded by Richard Daystrom...and Lastly the USS Enterprise commanded by myself, Admiral Pike." There was a tiny bit of a gasp in the air followed by the quiet murmur of everyone going to their neighbor asking why The Enterprise had so suddenly changed its captain. Up until at least yesterday, Captain Kirk had been captain, I mean he was the sole reason why Katie even wanted to go on to the Enterprise. I looked back at her and she was broken, you could see it on her face. Poor Katie, I thought, Poor, poor Katie.

As they started to call the names for graduation, the murmurs settled down and an atmosphere of anxious waiting and anticipation filled the air. On after the other was called, it must have been past 6 when we finally got to the H's. Then I saw him again. Him, who shared my sanctuary, him whose name I still don't know, him who I really should just forget for the best. "Riley O'Connor...Medical assistant...The USS Enterprise." It took me about four minutes to connect the words and then the face and then the recent events. Riley was his name...Riley had been in my classes since we were little...Riley O'Connor was in the same classes with me throughout our studies, and I hadn't even known his name...Riley O'Connor was going to be working with me.

As I processed my incapability of noticing people who have literally been with with me for most of my life, and the rather happy thought that I might get to know him. Though after all I had nearly a life time too….

"Lily James, Lily James?" I was awoken from my trance as the girl sitting to my right nudged me. With horrible clumsiness, I stumbled to my feet and tried to walk in my ridiculous high heels._ Heel toe, Heel toe_. It took me about seven unbearable minutes to reach the podium. Seven horrible, awkward minutes full of silence, as they refused to say my ship until I was handed my diploma. Admiral Pike looked at me with a twinkle in his eyes as Spock, who looked like he was trying to sole a very difficult puzzle while constipated, handed me my diploma. "Lily James, second in command medical chief, on the USS Enterprise."

Ho-ly Fuck. I stood there frozen, my hand gripping the diploma, and jaw blatantly open. Medical chief? How is that even possible? Spock tried to shake me from my trance my freeing his hand from our prolonged handshake. But yet I still stood there waiting for them to realize their mistake and put me in a ship more deserving with a job more fitting. "Lily, walk off the stage," Spock tried to wisher under his breath. "uh-huh, Right…ya ok.." I then with the stumbling awestricken movements, that were now clearly identified with my name, I walked off the stage and slumped into my seat. Medical fucking Chief, shit. Those were my basic thoughts through the next alphabetical half of the class. When we finally processed out onto the front campus, decorated with blooming cherry trees, it sank in.

Somehow Katie managed to break the neat lines and joined me with a smile that lit up her face. She too had been assigned to the Enterprise. She took one look at me and just started laughing, a pure joyous laugh. I had know choice to join in. Next thing I knew I was next to Leah and Luke in a sea of white graduation gowns smiling and laughing as if nothing even mattered anymore. I looked out into the white satin sea and meet eyes with none other than Riley O'Connor. He smiled and gave me a gentlemanly nod with his graduation cap before he took it off and threw it through the air. My last memory of Starfleet academy would be the rise of white caps into bright blue skies.

As promised we Luke and Leah meet us at our door. Leah was dressed in a red flowing dress with black heels. Luke matched her perfectly with a black and with suit with a classic red tie. Katie as always, wore something a little too scandoulas and reveling for the likes of a classy rich kid party. I, on the other hand, wore a fitted gold dress made up of parceling jewels. It would look like I belonged in the wealthy apparent building, where the party was being held.

We walked up to the skyscraper undisappointed. It escaped far into the clouds, testing the limits of possibilities. It was made of some sort of reflective glass, so if you happened to walk past, you might not even realize it was there. On the sides were massive willow trees genetically engineered red to fit the name of the Phoenix SkyScraper. The leaves swayed slightly in the night's breeze.

As we walked up, we heard a hushed arguing near the willow tree to the right. As I stepped closer I realized it was non other than Riley, "Um, Riley?. I'll meet you guys inside," I said as I walked closer to the whispers. When I got closer I realized it wasn't just Riley, but a small girl probably a few years younger than me. "Lily! Ah uh, um.." Thats when I realized, this was probably his girlfriend, my heart seemed to drop a little bit. How could I be so stupid! I didn't even know his name until earlier today. "Oh sorry, I…sorry," I mumbled an apology as I stepped away. "No wait!," he called after me. This is ah, this is my sister Amy." My heart bounced up a greater hight then before, like it was on some side of roller coaster. "Oh!" the surprise must have shown on my face, as he continued to explain. "She decided it was okay for her to come to a Senior party, even though she'll be an incoming freshmen next year."

Amy, a petite girl with light blond hair, had a look of permeant stubbornness on her face. "Its really no big deal. Mom said it was okay." Riley rubbed his face as if he was really getting tired of this argument. "No she said it was okay to come with me tomorrow, not to this party. You need to go home, now. Let's go." I suddenly realized that if she was going, then he was going with her. "Wait!" They both looked around like I was some crazy hobo who just made a prophecy about the end of the world. "I ah know someone who lives here…And I think if she wanted, Amy could stay in that apartment. Its to late to take her home, plus there are guards surrounding all exits to this place, trying to catch anyone under the influence." I could see Riley thinking it over weighing the consequences if he left, probably his little sister ratting on him. "Fine," Amy let out a little squeak, "but I swear if I see you doing anything, even if your on the same floor as the party, I'll take you straight home.

I managed to get a room using my parent's name. There were some upsides to having heartless money bags as parents. We left Amy totally content with free food service, a great view of the city, and of course pay per view. Then arm and arm we waked up to the party.

**Sorry for the cliffhanger, I didn't want it to end like that but I want the party and other tid bits to be in another chapter. So tell me what you think of Riley and Lily, yes? no? I will be adding so new characters on the Enterprise so keep that in mind. Any other comments about the story you can message me and if you review this I will check out your stories and review them. And if you like Percy Jackson/Demigods/Thor/Loki/Norse Mythology you can read my friends twist on the Percy Jackson series** s/10123610/1/New-Asgard

**New chapter Friday!**


	3. Chapter 3

**I kept my promise! I mean sure its only an hour to Saturday but right now it's still Friday. So yay I did that. Also I really really really hated last chapter and will defiantly update it some time so look out for that. In apology of that last chapter I tried to make this one really good, and to be honest I am really proud of it. So don't forget to read and review and Enjoy!**

Its a very weird feeling to walk into a room that has more money than you yourself will probably make in your lifetime. And I just did. We waked into what must have been the foyer. There were two stair cases that turned away from the door. And on the stair cases were gold leaf railings and white marble steps. Above your heads was a huge dome that would have put Rome to shame. And of course there was a lot of beer. There was possibly a years supplies of all types of alcohol, that no frat boy could attempt to finish, though they were trying.

I step forward smiling in wonder of it all. I turned around to Riley, "Well aren't you coming?" There was a sparkle in her eyes that out shown her dress, and the riches around her, and was positively absolutely irresistible. He answered with a smile, "Of course."

We half ran all half skipped like little kids all over the apartment until we saw someone familiar. In the kitchen, a master chef's culinary dream, we found Katie, a girl named Jenny, and three other boys were playing strip poker. Th three boys were down to their boxers and the two girls had a manageable three socks and two pairs of shoes lost. "Ha hey Katie, Going well?" I leaned down and whispered, "the guy on the left has two jacks and nothin' else." The girl, Jenny, called "all right I fold, show your cards." Katie with a siren's smirk called, "I win! come on James…" The guy on the left, presumably James, got to his feet, "Wait no she cheated, I saw you!" He was then jeered on by the other guys at the table, while chuckling, Riley ushered me away.

We landed next to the keg, and instinctively started pouring both of us a glass. "Woah wait," Riley started to say as he looked at the glass nervously. "Aw come on," I said, "relax you've finally made it. You can afford one drink." Riley still looked doubtful but he took it anyway. "So," I asked, "What should we do?" I could see the idea form in his head as the sparkle in his eyes matched the smile on his face, like the first time I really meet him, "Well, were on top of the world, I guess we should just enjoy the view."

He lead me through a couple of smokey rooms, one with some people who really seemed to enjoy the old re-runs of Friends. We arrived in what must have been the south end of the apartment. It was a huge space with about a dozen people playing pool in one end and a work area in the other separated by a large bookcase, all in front of a wall made of glass. He moved to the work side of the room where there was less people and pulled the desk to the window. He then climbed onto it sitting Indian style, and patted the side next to him. Willing to hear his words of wisdom, and escape the party scene around me, I climbed up next to him.

"Its kinda cool if you think about it," he started off saying. "Oh yeah," I said humoring him, "Why's that?" He gave me a side wise glance, as if saying "yeah I'm sure you do." He then turned his attention towards the city and mindlessly played with the fingers of my hand, "There must be a million people out there, I would say about 10 people know about us, family excluded." I let my head rest on his shoulder, "Yes quite possibly…but I feel as if I have more stalkers than that." He laughed at that and gave me another sidewise glance, "Ok well say 15. Now they could be having the best fuckin' days of their life. They finished an essay they were working on for a year, got a promotion, asked a really pretty girl out." He paused to smirk and allow enough time for me to nudge him. "Then theres a few out there who probably didn't have such a great day. Maybe the just lost their job, or their favorite team just lost, or even if they eat some really bad sushi." I rolled my eyes, "Yes theres a lot of people out there, but thats just it. That's the romanticism of cities. There's a thousand stories but only a few see the light. So what exactly is your point?" He seemed like a professor looking at me. Like he was teaching a lesson that I just couldn't get. "My point is, our story is gonna be told." And with that declaration he kissed me. In that moment those stories didn't matter. Sure a person could have a great day, they could have just become CEO, could have finished the next great American novel, could shave just married a super model, but nothing could be better than Riley O'Connor kissing me.

But then it all changed. Worse then losing your high paying job, worse then having your favorite team disbanded, worse then eat week old sushi. I heard it when the gasps, and "oh my gods" and the quiet sobs started. I felt it like a ripple through my bones. I saw it in a horribly beautiful act of chaos. Section 31 was falling. No it was't bad structure, or too old. It was falling because there was a fiery eruption was pouring out of its base. No one realized the possible scope of the casualties at the moment. What we saw were those horrible days and those good days all put to an end forever.

At the same moment the Section 31 building collapsed, a tall man of an unknown race, alien or otherwise, entreated the Phoenix Apartment Building. He told the kind lady at the desk that his name was John James, father of Lily James, and wanted to stay in their rented suite with her for the night. The receptionist kindly obliged and gave him an extra key for good measure. The tall mysterious man in the trench coat road the elevator to the 134th suite. He then stepped out and put his key to the door, to find 'Lily James' asleep on the couch with an old episode of Saturday Night Live Playing. He then took a tranquilizer gun from the pockets of his coat and shot 'Lily James' in the neck from twenty feet away. Placing the tranquilizer gun back into his pocket, he took out what looked like car keys to the normal eye and a phaser gun. He shot the gun at the glass window behind 'Lily James.' It shattered to tiny shards, mostly falling on the poor citizens below. He then pressed the car keys which altered his ship and sent it to great him at the broken window. The man in the trench coat took long deliberate strides towards 'Lily James' and picked her up bridal style. He then continued his long strides before jumping into his ship with 'Lily James," aka Amy O'Connor.

**Yup so thats it probably another chapter Sunday, though I may break that promise. If you like it you can always press that follow/favorite button and make my day! And if you hate it, or hate Riley and Lily, or if I wrote bad dialogue, or just want to complain about your bad sushi day just comment, or review and I will get back to you and review/comment your stories!**


End file.
